Question

I have pretty simple problem. I have a large file that goes through three steps, a decoding step using an external program, some processing in python, and then recoding using another external program. I have been using subprocess.Popen() to try to do this in python rather than forming unix pipes. However, all the data are buffered to memory. Is there a pythonic way of doing this task, or am I best dropping back to a simple python script that reads from stdin and writes to stdout with unix pipes on either side?

import os, sys, subprocess

def main(infile,reflist):
    print infile,reflist
    samtoolsin = subprocess.Popen(["samtools","view",infile],
                                  stdout=subprocess.PIPE,bufsize=1)
    samtoolsout = subprocess.Popen(["samtools","import",reflist,"-",
                                    infile+".tmp"],stdin=subprocess.PIPE,bufsize=1)
    for line in samtoolsin.stdout.read():
        if(line.startswith("@")):
            samtoolsout.stdin.write(line)
        else:
            linesplit = line.split("\t")
            if(linesplit[10]=="*"):
                linesplit[9]="*"
            samtoolsout.stdin.write("\t".join(linesplit))

Answer 1

Popen has a bufsize parameter that will limit the size of the buffer in memory. If you don’t want the files in memory at all, you can pass file objects as the stdin and stdout parameters. From the subprocess docs:

bufsize, if given, has the same meaning as the corresponding argument to the built-in open() function: 0 means unbuffered, 1 means line buffered, any other positive value means use a buffer of (approximately) that size. A negative bufsize means to use the system default, which usually means fully buffered. The default value for bufsize is 0 (unbuffered).